Little Book of R for Bioinformatics by Avril Coghlan

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Introduction to bioinformatics, with a focus on genome analysis, using the R statistics software. By Avril Coghlan(Wellcome Trust Sanger Institute, Cambridge,UK). 

To encourage research into neglected tropical diseases such as leprosy, Chagas disease, trachoma, schistosomiasis etc., most of the examples in this booklet are for analysis of the genomes of the organisms that cause these diseases.
The author booklet on using R for biomedical statistics, http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/, and booklet on using R for time series analysis, http://a-little-book-of-r-for-time-series.readthedocs.org/.

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